Monodispersed CdTe(x)Se1-x and CdSe cores were synthesized via organic methods. The as-prepared cores were coated with a Cd(y)Zn1-yS shell by an epitaxial growth. Compared with the cores, an obvious red shift was observed in both the absorption and photoluminescence (PL) spectra of core-shell quantum dots (QDs) and the PL efficiency was improved. The CdSe-based core-shell QDs were transferred from oil to water phase by the encapsulation of amphiphilic polymers. The ligands of QDs, namely hexadecylamine (HDA) and oleic acid (OA), dramatically influenced the process of phase transfer. The process of phase transfer of HDA-coated CdTe(x)Se1-x/CdyZn1-yS core-shell QDs was failed, however, the OA-coated CdSe/CdyZn1-yS core-shell QDs can be successfully transferred from oil to water phase. This is ascribed that the surface ligand HDA falls from CdTe(x)Se1-x/Cd(y)Zn1-yS core-shell QDs during the process of phase transfer, leading to non-interaction between QDs and amphiphilic polymers. The effect of molecular weight of the poly(styrene-co-maleic anhydride) (PSMA) on the phase transfer was also investigated. For the QDs with the same size, the PSMA with high molecular weight exhibit a shorter time in the process of phase transfer compared with light molecular weight. Furthermore, the size of the QDs also affects the process of the phase transfer from oil to water phase. The smaller of the QDs, the shorter of the phase transfer time.